During microbial growth, changes in the environmental conditions are accompanied by corresponding alterations in microbial gene expression, metabolites, proteins as well as regulation of enzyme activity. To reveal gene-phenotype relationships, it is important to gain insights into the complex microbial global regulatory process in its entirety. We have profiled the genome-wide expression of metal-reducing microbe, Shewanella oneidensis MR-1 in over 200 different environmental conditions using Affymetrix microarray platform for Shewanella. We applied the Context-likelihood of Relatedness algorithm on this expression compendium to infer the first full-scale regulatory network for S. oneidensis MR-1. The resultant network showed several previously uncharacterized genes as central regulators of the respiratory machinery. This first ever large-scale map of S. oneidensis transcriptome revealed a tightly regulated core of respiratory enzymes, co-factor synthesis proteins, and molecular chaperones, which appears to support this organism's signature respiratory capabilities. Our map also showed several novel regulators as potential mediators of anaerobic respiration. These regulators may represent useful targets for altering S. oneidensis's capacity for electron transport onto metals. To further gain insights into the complex global transcriptional regulatory process in S. oneidensis, currently we are conducting more growth experiments in batch and continuous cultures in both complex and lactate-limited minimal media. The collected biomass samples at several different times are subjected to microarray analysis to look for up-, and down-regulation of gene signatures and transcriptional programs during S. oneidensis growth in exponential, stationary phase, and steady-state cells.